3MF5

Hepatitis C virus polymerase NS5B (BK) with amide bioisostere thumb site inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Cyclic amide bioisosterism: Strategic application to the design and synthesis of HCV NS5B polymerase inhibitors.

Yang, H., Hendricks, R.T., Arora, N., Nitzan, D., Yee, C., Lucas, M.C., Yang, Y., Fung, A., Rajyaguru, S., Harris, S.F., Leveque, V.J., Hang, J.Q., Pogam, S.L., Reuter, D., Tavares, G.A.

(2010) Bioorg Med Chem Lett 20: 4614-4619

  • DOI: 10.1016/j.bmcl.2010.06.008
  • Primary Citation of Related Structures:  
    3MF5

  • PubMed Abstract: 

    • Conformational modeling has been successfully applied to the design of cyclic bioisosteres used to replace a conformationally rigid amide bond in a series of thiophene carboxylate inhibitors of HCV NS5B polymerase. Select compounds were equipotent with the original amide series ...

    Conformational modeling has been successfully applied to the design of cyclic bioisosteres used to replace a conformationally rigid amide bond in a series of thiophene carboxylate inhibitors of HCV NS5B polymerase. Select compounds were equipotent with the original amide series. Single-point mutant binding studies, in combination with inhibition structure-activity relationships, suggest this new series interacts at the Thumb-II domain of NS5B. Inhibitor binding at the Thumb-II site was ultimately confirmed by solving a crystal structure of 8b complexed with NS5B.

    Organizational Affiliation: 

    Medicinal Chemistry Department, Roche Palo Alto, LLC, Palo Alto, CA 94304, USA. Hanbiaoyang@gmail.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B570Hepatitis C virus (isolate BK)Mutation(s): 0 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJZ
Query on HJZ
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		3-[2-(trans-4-methylcyclohexyl)phenyl]-5-phenylthiophene-2-carboxylic acid
C24 H24 O2 S
XAWPFEPCAOCGHU-QAQDUYKDSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HJZ PDBBind:  3MF5 Kd: 4320 (nM) from 1 assay(s)
Binding MOAD:  3MF5 IC50: 42 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.447α = 90
b = 105.363β = 90
c = 126.119γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance